+ set -e + /usr/bin/time -v sourmash gather --no-linear --prefetch out.sig gtdb-rs202.genomic-reps.k31.zip overlap p_query p_match avg_abund --------- ------- ------- --------- 2.7 Mbp 42.0% 100.0% 1.0 GCF_000746205.1 Halorubrum sp. BV1 st... 2.3 Mbp 35.5% 100.0% 1.0 GCA_002498315.1 Methanofollis sp. UBA... 0.8 Mbp 12.5% 100.0% 1.0 GCA_902514095.1 uncultured marine gro... 0.7 Mbp 10.0% 100.0% 1.0 GCA_002688395.1 Nanoarchaeota archaeo... found 4 matches total; the recovered matches hit 100.0% of the query  == This is sourmash version 4.0.1.dev37+gad03e1ec. == == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. == select query k=31 automatically. loaded query: d52ec062... (k=31, DNA) loading from gtdb-rs202.genomic-reps.k31.zip...  loaded 1 databases. Starting prefetch sweep across databases. Found 26 signatures via prefetch; now doing gather. Command being timed: "sourmash gather --no-linear --prefetch out.sig gtdb-rs202.genomic-reps.k31.zip" User time (seconds): 207.58 System time (seconds): 2.27 Percent of CPU this job got: 100% Elapsed (wall clock) time (h:mm:ss or m:ss): 3:27.96 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 Maximum resident set size (kbytes): 81284 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 19 Minor (reclaiming a frame) page faults: 29468 Voluntary context switches: 1401 Involuntary context switches: 353174 Swaps: 0 File system inputs: 770360 File system outputs: 16 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0 + /usr/bin/time -v sourmash gather --linear --prefetch out.sig gtdb-rs202.genomic-reps.k31.zip overlap p_query p_match avg_abund --------- ------- ------- --------- 2.7 Mbp 42.0% 100.0% 1.0 GCF_000746205.1 Halorubrum sp. BV1 st... 2.3 Mbp 35.5% 100.0% 1.0 GCA_002498315.1 Methanofollis sp. UBA... 0.8 Mbp 12.5% 100.0% 1.0 GCA_902514095.1 uncultured marine gro... 0.7 Mbp 10.0% 100.0% 1.0 GCA_002688395.1 Nanoarchaeota archaeo... found 4 matches total; the recovered matches hit 100.0% of the query  == This is sourmash version 4.0.1.dev37+gad03e1ec. == == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. == select query k=31 automatically. loaded query: d52ec062... (k=31, DNA) loading from gtdb-rs202.genomic-reps.k31.zip...  loaded 1 databases. Starting prefetch sweep across databases. Found 26 signatures via prefetch; now doing gather. Command being timed: "sourmash gather --linear --prefetch out.sig gtdb-rs202.genomic-reps.k31.zip" User time (seconds): 205.74 System time (seconds): 2.41 Percent of CPU this job got: 101% Elapsed (wall clock) time (h:mm:ss or m:ss): 3:25.15 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 Maximum resident set size (kbytes): 81152 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 29433 Voluntary context switches: 1951 Involuntary context switches: 159585 Swaps: 0 File system inputs: 0 File system outputs: 16 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0 + /usr/bin/time -v sourmash gather --no-linear --no-prefetch out.sig gtdb-rs202.genomic-reps.k31.zip overlap p_query p_match avg_abund --------- ------- ------- --------- 2.7 Mbp 42.0% 100.0% 1.0 GCF_000746205.1 Halorubrum sp. BV1 st... 2.3 Mbp 35.5% 100.0% 1.0 GCA_002498315.1 Methanofollis sp. UBA... 0.8 Mbp 12.5% 100.0% 1.0 GCA_902514095.1 uncultured marine gro... 0.7 Mbp 10.0% 100.0% 1.0 GCA_002688395.1 Nanoarchaeota archaeo... found 4 matches total; the recovered matches hit 100.0% of the query  == This is sourmash version 4.0.1.dev37+gad03e1ec. == == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. == select query k=31 automatically. loaded query: d52ec062... (k=31, DNA) loading from gtdb-rs202.genomic-reps.k31.zip...  loaded 1 databases. Command being timed: "sourmash gather --no-linear --no-prefetch out.sig gtdb-rs202.genomic-reps.k31.zip" User time (seconds): 811.41 System time (seconds): 3.77 Percent of CPU this job got: 100% Elapsed (wall clock) time (h:mm:ss or m:ss): 13:31.40 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 Maximum resident set size (kbytes): 87284 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 100851 Voluntary context switches: 1720 Involuntary context switches: 531 Swaps: 0 File system inputs: 0 File system outputs: 48 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0 + /usr/bin/time -v sourmash gather --linear --no-prefetch out.sig gtdb-rs202.genomic-reps.k31.zip overlap p_query p_match avg_abund --------- ------- ------- --------- 2.7 Mbp 42.0% 100.0% 1.0 GCF_000746205.1 Halorubrum sp. BV1 st... 2.3 Mbp 35.5% 100.0% 1.0 GCA_002498315.1 Methanofollis sp. UBA... 0.8 Mbp 12.5% 100.0% 1.0 GCA_902514095.1 uncultured marine gro... 0.7 Mbp 10.0% 100.0% 1.0 GCA_002688395.1 Nanoarchaeota archaeo... found 4 matches total; the recovered matches hit 100.0% of the query  == This is sourmash version 4.0.1.dev37+gad03e1ec. == == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. == select query k=31 automatically. loaded query: d52ec062... (k=31, DNA) loading from gtdb-rs202.genomic-reps.k31.zip...  loaded 1 databases. Command being timed: "sourmash gather --linear --no-prefetch out.sig gtdb-rs202.genomic-reps.k31.zip" User time (seconds): 802.00 System time (seconds): 4.59 Percent of CPU this job got: 100% Elapsed (wall clock) time (h:mm:ss or m:ss): 13:23.54 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 Maximum resident set size (kbytes): 86772 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 100982 Voluntary context switches: 1902 Involuntary context switches: 272646 Swaps: 0 File system inputs: 0 File system outputs: 40 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0 + /usr/bin/time -v sourmash gather --no-linear --prefetch out.sig gtdb-rs202.genomic-reps.k31.sbt.zip overlap p_query p_match avg_abund --------- ------- ------- --------- 2.7 Mbp 42.0% 100.0% 1.0 GCF_000746205.1 Halorubrum sp. BV1 st... 2.3 Mbp 35.5% 100.0% 1.0 GCA_002498315.1 Methanofollis sp. UBA... 0.8 Mbp 12.5% 100.0% 1.0 GCA_902514095.1 uncultured marine gro... 0.7 Mbp 10.0% 100.0% 1.0 GCA_002688395.1 Nanoarchaeota archaeo... found 4 matches total; the recovered matches hit 100.0% of the query  == This is sourmash version 4.0.1.dev37+gad03e1ec. == == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. == select query k=31 automatically. loaded query: d52ec062... (k=31, DNA) loading from gtdb-rs202.genomic-reps.k31.sbt.zip...  loaded 1 databases. Starting prefetch sweep across databases. Found 26 signatures via prefetch; now doing gather. Command being timed: "sourmash gather --no-linear --prefetch out.sig gtdb-rs202.genomic-reps.k31.sbt.zip" User time (seconds): 10.92 System time (seconds): 3.56 Percent of CPU this job got: 128% Elapsed (wall clock) time (h:mm:ss or m:ss): 0:11.27 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 Maximum resident set size (kbytes): 215292 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 68171 Voluntary context switches: 1911 Involuntary context switches: 195528 Swaps: 0 File system inputs: 0 File system outputs: 23592 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0 + /usr/bin/time -v sourmash gather --linear --prefetch out.sig gtdb-rs202.genomic-reps.k31.sbt.zip overlap p_query p_match avg_abund --------- ------- ------- --------- 2.7 Mbp 42.0% 100.0% 1.0 GCF_000746205.1 Halorubrum sp. BV1 st... 2.3 Mbp 35.5% 100.0% 1.0 GCA_002498315.1 Methanofollis sp. UBA... 0.8 Mbp 12.5% 100.0% 1.0 GCA_902514095.1 uncultured marine gro... 0.7 Mbp 10.0% 100.0% 1.0 GCA_002688395.1 Nanoarchaeota archaeo... found 4 matches total; the recovered matches hit 100.0% of the query  == This is sourmash version 4.0.1.dev37+gad03e1ec. == == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. == select query k=31 automatically. loaded query: d52ec062... (k=31, DNA) loading from gtdb-rs202.genomic-reps.k31.sbt.zip...  loaded 1 databases. Starting prefetch sweep across databases. Found 26 signatures via prefetch; now doing gather. Command being timed: "sourmash gather --linear --prefetch out.sig gtdb-rs202.genomic-reps.k31.sbt.zip" User time (seconds): 177.54 System time (seconds): 3.45 Percent of CPU this job got: 102% Elapsed (wall clock) time (h:mm:ss or m:ss): 2:57.26 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 Maximum resident set size (kbytes): 1502204 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 391543 Voluntary context switches: 1161 Involuntary context switches: 55266 Swaps: 0 File system inputs: 0 File system outputs: 23592 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0 + /usr/bin/time -v sourmash gather --no-linear --no-prefetch out.sig gtdb-rs202.genomic-reps.k31.sbt.zip overlap p_query p_match avg_abund --------- ------- ------- --------- 2.7 Mbp 42.0% 100.0% 1.0 GCF_000746205.1 Halorubrum sp. BV1 st... 2.3 Mbp 35.5% 100.0% 1.0 GCA_002498315.1 Methanofollis sp. UBA... 0.8 Mbp 12.5% 100.0% 1.0 GCA_902514095.1 uncultured marine gro... 0.7 Mbp 10.0% 100.0% 1.0 GCA_002688395.1 Nanoarchaeota archaeo... found 4 matches total; the recovered matches hit 100.0% of the query  == This is sourmash version 4.0.1.dev37+gad03e1ec. == == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. == select query k=31 automatically. loaded query: d52ec062... (k=31, DNA) loading from gtdb-rs202.genomic-reps.k31.sbt.zip...  loaded 1 databases. Command being timed: "sourmash gather --no-linear --no-prefetch out.sig gtdb-rs202.genomic-reps.k31.sbt.zip" User time (seconds): 22.63 System time (seconds): 6.73 Percent of CPU this job got: 114% Elapsed (wall clock) time (h:mm:ss or m:ss): 0:25.61 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 Maximum resident set size (kbytes): 214764 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 130318 Voluntary context switches: 1714 Involuntary context switches: 172 Swaps: 0 File system inputs: 0 File system outputs: 23600 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0 + /usr/bin/time -v sourmash gather --linear --no-prefetch out.sig gtdb-rs202.genomic-reps.k31.sbt.zip overlap p_query p_match avg_abund --------- ------- ------- --------- 2.7 Mbp 42.0% 100.0% 1.0 GCF_000746205.1 Halorubrum sp. BV1 st... 2.3 Mbp 35.5% 100.0% 1.0 GCA_002498315.1 Methanofollis sp. UBA... 0.8 Mbp 12.5% 100.0% 1.0 GCA_902514095.1 uncultured marine gro... 0.7 Mbp 10.0% 100.0% 1.0 GCA_002688395.1 Nanoarchaeota archaeo... found 4 matches total; the recovered matches hit 100.0% of the query  == This is sourmash version 4.0.1.dev37+gad03e1ec. == == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. == select query k=31 automatically. loaded query: d52ec062... (k=31, DNA) loading from gtdb-rs202.genomic-reps.k31.sbt.zip...  loaded 1 databases. Command being timed: "sourmash gather --linear --no-prefetch out.sig gtdb-rs202.genomic-reps.k31.sbt.zip" User time (seconds): 187.44 System time (seconds): 3.79 Percent of CPU this job got: 102% Elapsed (wall clock) time (h:mm:ss or m:ss): 3:07.48 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 Maximum resident set size (kbytes): 1505020 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 746722 Voluntary context switches: 935 Involuntary context switches: 55624 Swaps: 0 File system inputs: 0 File system outputs: 23600 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0